Compton, AustinLiang, JiangtaoChen, ChujiaLukyanchikova, VarvaraQi, YuminPotters, Mark B.Settlage, RobertMiller, DustinDeschamps, StephaneMao, ChunhongLlaca, VictorSharakhov, Igor V.Tu, Zhijian Jake2021-01-212021-01-212020-10-012160-1836g3.120.401654 (PII)http://hdl.handle.net/10919/101986Chromosome level assemblies are accumulating in various taxonomic groups including mosquitoes. However, even in the few reference-quality mosquito assemblies, a significant portion of the heterochromatic regions including telomeres remain unresolved. Here we produce a de novo assembly of the New World malaria mosquito, Anopheles albimanus by integrating Oxford Nanopore sequencing, Illumina, Hi-C and optical mapping. This 172.6 Mbps female assembly, which we call AalbS3, is obtained by scaffolding polished large contigs (contig N50 = 13.7 Mbps) into three chromosomes. All chromosome arms end with telomeric repeats, which is the first in mosquito assemblies and represents a significant step toward the completion of a genome assembly. These telomeres consist of tandem repeats of a novel 30-32 bp Telomeric Repeat Unit (TRU) and are confirmed by analyzing the termini of long reads and through both chromosomal in situ hybridization and a Bal31 sensitivity assay. The AalbS3 assembly included previously uncharacterized centromeric and rDNA clusters and more than doubled the content of transposable elements and other repetitive sequences. This telomere-to-telomere assembly, although still containing gaps, represents a significant step toward resolving biologically important but previously hidden genomic components. The comparison of different scaffolding methods will also inform future efforts to obtain reference-quality genomes for other mosquito species.Pages 3811-38199 page(s)application/pdfenCreative Commons Attribution 4.0 InternationalLife Sciences & BiomedicineGenetics & HeredityGenome assemblyAnopheles albimanusOxford NanoporeHi-CBionanoANOPHELES-ALBIMANUSDROSOPHILA-MELANOGASTERELONGATIONSEQUENCESREPEATLENGTHDNA0604 GeneticsArticle - Refereed2021-01-21https://doi.org/10.1534/g3.120.4016541010Sharakhov, Igor [0000-0003-0752-3747]Liang, Jiangtao [0000-0002-8468-7457]Tu, Zhijian [0000-0003-4227-3819]32883756 (pubmed)2160-1836